stopCodons: Get the Stop codons (3 bases) from a GRangesList of orfs...

In JokingHero/ORFik: Open Reading Frames in Genomics

Get the Stop codons (3 bases) from a GRangesList of orfs grouped by orfs

Description

In ATGTTTTGA, get the positions TGA. It takes care of exons boundaries, with exons < 3 length.

Usage

stopCodons(grl, is.sorted = FALSE)

Arguments

grl	a GRangesList object
is.sorted	a boolean, a speedup if you know the ranges are sorted

Value

a GRangesList of stop codons, since they might be split on exons

See Also

Other ORFHelpers: defineTrailer(), longestORFs(), mapToGRanges(), orfID(), startCodons(), startSites(), stopSites(), txNames(), uniqueGroups(), uniqueOrder()

Examples

gr_plus <- GRanges(seqnames = c("chr1", "chr1"),
                   ranges = IRanges(c(7, 14), width = 3),
                   strand = c("+", "+"))
gr_minus <- GRanges(seqnames = c("chr2", "chr2"),
                    ranges = IRanges(c(4, 1), c(9, 3)),
                    strand = c("-", "-"))
grl <- GRangesList(tx1 = gr_plus, tx2 = gr_minus)
stopCodons(grl, is.sorted = FALSE)

JokingHero/ORFik documentation built on Oct. 21, 2024, 11:42 a.m.